Yeah, I didn't catch it at first. So 3DS owners get Duck Hunt instead, that's cool.
This also sets a precedent for future stages.
We got the first paid DLC exclusive to one version (seems that any new stages will always be on both versions tho), first stage ported between games (we could see others maybe in the future, but probably only if they evenly exchange the number of stages), first stage(s) to use music tracks on already existing content, not just 64 returning stages.
We could potentially see a lot of "past" stages on Wii U and 3DS shift between versions now, and maybe some exclusive ones like Magicant and Mute City. However, most likely, the stages will only be ported over if there's an even exchange.
This probably decreases the likelihood of seeing Kongo Jungle Melee, though, and other stages like that, and instead they'd shift stages between versions. Say, an even exchange of Jungle Japes and Kongo Jungle 64. Or if we get other Wii U exclusive DLC stages, such as New Pork City (this one is a likely candidate for being Wii U exclusive), we could get another Wii U stage shifted over to 3DS.